def main(argv): """"Convert a directory of tifs to an hdf5 stack.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_series2stack(parser) parser = parse.parse_common(parser) args = parser.parse_args() series2stack( args.inputdir, args.regex, args.element_size_um, args.outlayout, args.datatype, args.chunksize, args.dataslices, args.usempi & ('mpi4py' in sys.modules), args.outputformats, args.outputpath, args.save_steps, args.protective, )
def main(argv): """Fill holes in labels.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_fill_holes(parser) parser = parse.parse_common(parser) args = parser.parse_args() fill_holes( args.inputfile, args.methods, args.selem, args.labelmask, args.maskDS, args.maskMM, args.maskMX, args.outputfile, args.outputholes, args.outputMA, args.outputMM, args.protective, )
def main(argv): """Delete/split/merge/... labels in a labelvolume.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_remap_labels(parser) parser = parse.parse_common(parser) args = parser.parse_args() remap_labels( args.inputfile, args.delete_labels, args.delete_files, args.except_files, args.merge_labels, args.merge_files, args.split_labels, args.split_files, args.aux_labelvolume, args.min_labelsize, args.min_segmentsize, args.keep_only_largest, args.conncomp, args.nifti_output, args.nifti_transpose, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Convert/select/downscale/transpose/... an hdf5 dataset.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_stack2stack(parser) parser = parse.parse_common(parser) args = parser.parse_args() stack2stack( args.inputfile, args.outputfile, args.dset_name, args.blockoffset, args.datatype, args.uint8conv, args.inlayout, args.outlayout, args.element_size_um, args.chunksize, args.additional_outputs, args.nzfills, args.dataslices, args.save_steps, args.protective, )
def main(argv): """Find labels that do not traverse through the volume.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_nodes_of_ranvier(parser) parser = parse.parse_common(parser) args = parser.parse_args() nodes_of_ranvier( args.inputfile, args.min_labelsize, args.remove_small_labels, args.boundarymask, args.merge_methods, args.overlap_threshold, args.data, args.maskMM, args.searchradius, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Merge blocks of data into a single hdf5 dataset.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser = parse.parse_mergeblocks(parser) parser = parse.parse_common(parser) args = parser.parse_args() mergeblocks( args.inputfiles, args.blockoffset, args.blocksize, args.margin, args.fullsize, args.is_labelimage, args.relabel, args.neighbourmerge, args.save_fwmap, args.blockreduce, args.func, args.datatype, args.usempi & ('mpi4py' in sys.modules), args.outputfile, args.save_steps, args.protective, )
def main(argv): """Merge slice-wise overlapping labels.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_merge_slicelabels(parser) parser = parse.parse_common(parser) args = parser.parse_args() if args.mode == "MAstitch": evaluate_overlaps( args.inputfile, args.slicedim, args.offsets, args.threshold_overlap, args.do_map_labels, args.maskMM, args.min_labelsize, args.close, args.relabel_from, args.usempi & ('mpi4py' in sys.modules), args.outputfile, args.save_steps, args.protective, ) elif args.mode == "MAfwmap": map_labels( args.inputfile, args.outputfile, args.save_steps, args.protective, ) elif args.mode == "MAfilter": filter_labels( args.inputfile, args.maskMM, args.min_labelsize, args.close, args.relabel_from, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Convert dm3 files to other image formats.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser = parse.parse_convert_dm3(parser) parser = parse.parse_common(parser) args = parser.parse_args() convert_dm3( args.inputdir, args.outputdir, args.save_steps, args.protective, )
def main(argv): """Correct attributes of a h5 dataset.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_correct_attributes(parser) parser = parse.parse_common(parser) args = parser.parse_args() correct_attributes( args.inputfile, args.auxfile, args.outlayout, args.element_size_um, )
def main(argv): """Combine volumes by addition.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_combine_vols(parser) parser = parse.parse_common(parser) args = parser.parse_args() combine_vols( args.inputfile, args.volidxs, args.outputfile, args.protective, )
def main(argv): """Filter nodes of ranvier.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_filter_NoR(parser) parser = parse.parse_common(parser) args = parser.parse_args() filter_NoR( args.inputfile, args.input2D, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Compute segmentation statistics.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser = parse.parse_seg_stats(parser) parser = parse.parse_common(parser) args = parser.parse_args() seg_stats( args.h5path_labelMA, args.h5path_labelMF, args.h5path_labelUA, args.stats, args.outputbasename, args.protective, )
def main(argv): """Label connected components.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_connected_components_clf(parser) parser = parse.parse_common(parser) args = parser.parse_args() if args.mode == 'train': CC_clf_train( args.inputfile, args.outputfile, args.save_steps, args.protective, ) elif args.mode == 'test': CC_clf_test( args.classifierpath, args.scalerpath, args.basename, args.map_propnames, args.max_intensity_mb, args.max_area, args.inputfile, args.outputfile, args.maskfile, args.save_steps, args.protective, ) if args.mode == 'map': CC_clf_map( args.inputfile, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Apply mapping of labelsets to a labelvolume.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_agglo_from_labelmask(parser) parser = parse.parse_common(parser) args = parser.parse_args() agglo_from_labelmask( args.inpufile, args.labelvolume, args.ratio_threshold, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Downsample volume by blockwise reduction.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser = parse.parse_downsample_blockwise(parser) parser = parse.parse_common(parser) args = parser.parse_args() downsample_blockwise( args.inputfile, args.blockreduce, args.func, args.dataslices, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Downsample a series of 2D images.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_downsample_slices(parser) parser = parse.parse_common(parser) args = parser.parse_args() downsample_slices( args.inputdir, args.outputdir, args.regex, args.downsample_factor, args.dataslices, args.usempi & ('mpi4py' in sys.modules), args.protective, )
def main(argv): """"Convert a directory of tifs to an hdf5 stack.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser = parse.parse_splitblocks(parser) parser = parse.parse_common(parser) args = parser.parse_args() splitblocks( args.inputfile, args.dset_name, args.dataslices, args.blocksize, args.margin, args.blockrange, args.usempi & ('mpi4py' in sys.modules), args.outputdir, args.save_steps, args.protective, )
def main(argv): """Create thresholded hard segmentations.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser = parse.parse_prob2mask(parser) parser = parse.parse_common(parser) args = parser.parse_args() if args.step: for thr in frange(args.step, 1.0, args.step): prob2mask( args.inputfile, args.dataslices, thr, args.upper_threshold, args.size, args.dilation, args.inputmask, args.go2D, args.outputfile.format(thr), args.save_steps, args.protective, ) else: prob2mask( args.inputfile, args.dataslices, args.lower_threshold, args.upper_threshold, args.size, args.dilation, args.inputmask, args.go2D, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Perform watershed on the intracellular space compartments.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser = parse.parse_watershed_ics(parser) parser = parse.parse_common(parser) args = parser.parse_args() watershed_ics( args.inputfile, args.masks, args.seedimage, args.seed_size, args.lower_threshold, args.upper_threshold, args.invert, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Separate the myelin compartment into individual myelin sheaths.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser = parse.parse_separate_sheaths(parser) parser = parse.parse_common(parser) args = parser.parse_args() separate_sheaths( args.inputfile, args.labelMM, args.maskWS, args.maskDS, args.maskMM, args.dilation_iterations, args.distance, args.sigmoidweighting, args.margin, args.outputfile, args.save_steps, args.protective, )
def main(argv): """Label connected components.""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter ) parser = parse.parse_connected_components(parser) parser = parse.parse_common(parser) args = parser.parse_args() if args.mode == '3D': CC_3D( args.inputfile, args.maskDS, args.min_size_maskMM, args.min_area, args.outputfile, args.protective, ) elif args.mode == '2D': CC_2D( args.inputfile, args.maskDS, args.slicedim, args.usempi & ('mpi4py' in sys.modules), args.outputfile, args.protective, ) elif args.mode == "2Dfilter": criteria = ( args.min_area, args.max_area, args.max_intensity_mb, args.max_eccentricity, args.min_solidity, args.min_euler_number, args.min_extent ) CC_2Dfilter( args.inputfile, args.map_propnames, criteria, args.maskMB, args.slicedim, args.usempi & ('mpi4py' in sys.modules), args.outputfile, args.protective, ) elif args.mode == "2Dprops": CC_2Dprops( args.inputfile, args.basename, args.map_propnames, args.usempi & ('mpi4py' in sys.modules), args.outputfile, args.protective, ) elif args.mode == "2Dto3D": CC_2Dto3D( args.inputfile, args.outputfile, args.protective, )